[English] 日本語
Yorodumi
- PDB-1mt0: ATP-binding domain of hemolysin B from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mt0
TitleATP-binding domain of hemolysin B from Escherichia coli
ComponentsHemolysin secretion ATP-binding protein
KeywordsTRANSPORT PROTEIN / ABC-transporter / ATP-binding domain / Hemolysin B / ATP-dependent transport protein
Function / homology
Function and homology information


protein secretion by the type I secretion system / type I protein secretion system complex / : / toxin transmembrane transporter activity / secretion by cell / ABC-type transporter activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily ...ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSchmitt, L. / Benabdelhak, H. / Blight, M.A. / Holland, I.B. / Stubbs, M.T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of the nucleotide binding domain of the ABC-transporter hemolysin B: identification of a variable region within ABC helical domains
Authors: Schmitt, L. / Benabdelhak, H. / Blight, M.A. / Holland, I.B. / Stubbs, M.T.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin secretion ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0202
Polymers26,9241
Non-polymers961
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.2, 105.2, 125.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Hemolysin secretion ATP-binding protein


Mass: 26923.967 Da / Num. of mol.: 1 / Fragment: ATP-binding domain (residues 467-707)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HLYB / Plasmid: pPSG116 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: P08716
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal growTemperature: 277 K / pH: 6.25
Details: PEG 8000, ammonium sulfate, (2-acetamido)iminodiacetic acid, sodium phosphate, potassium chloride, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMsodium phosphate1droppH8.0
3100 mM1dropKCl
450 mMATP1droppH7.0
5150 mMdiamino acetic acid1reservoirpH6.2
616 %(w/v)PEG80001reservoir
7300 mMammonium sulfate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2MADMx-ray1
1MADMx-ray1
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / % possible obs: 97.3 % / Observed criterion σ(I): 1.5 / Redundancy: 5.2 % / Biso Wilson estimate: 54.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.76 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.349 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→16.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1429357.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2142 9.9 %RANDOM
Rwork0.234 ---
obs0.234 21577 97.3 %-
all-23587 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5621 Å2 / ksol: 0.317979 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.79 Å20 Å20 Å2
2--9.79 Å20 Å2
3----19.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.6→16.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 5 130 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.411.5
X-RAY DIFFRACTIONc_mcangle_it8.782
X-RAY DIFFRACTIONc_scbond_it8.382
X-RAY DIFFRACTIONc_scangle_it12.562.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 373 10.3 %
Rwork0.411 3244 -
obs--99.6 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more